I know each element of the central dogma is a code in the mathematical sense of finite-state machines. That is, DNA is transcribed into RNA, and RNA into proteins. What other examples are there of codes that exist naturally in organisms?
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asked Jan 3, 2015 at 2:17
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$\begingroup$ Developmental patterning(?) $\endgroup$– WYSIWYGCommented Jan 3, 2015 at 5:13
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$\begingroup$ Stepwise polymerization of monomers, Operons for catabolism, operons for anabolism. Inducible and Repressible genomic expressions. Your question is very general. Also, besides methods of mathematical analysis, central dogma is mathematical in what sense exactly ? $\endgroup$– Macedon93Commented Jan 3, 2015 at 7:19
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$\begingroup$ @Macedona93 I am no expert. However, I believe FSM theories define a particular class of mathematical objects related to what are known as free monoids. I believe the conversion of DNA to RNA or vice versa follows FSM processing of this type. I think this is a well-established fact and is really the true definition for what we casually call a "code". $\endgroup$– Stan ShunpikeCommented Jan 3, 2015 at 8:45
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$\begingroup$ I see, perhaps im not enlightened in Finite State Machines and their philosophical relaton to cell and molecular biology. I just know that the rules of cellular biology follow those of physics, biological thermodynamics (Free energies and what have you) amongst others. Like the fact that DNA is coded in respects to monomerical polymerization. Regardless, i up-voted the question as i find it quite interesting. Seriously check out operons, they're quite amazing. $\endgroup$– Macedon93Commented Jan 3, 2015 at 8:58
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DNA is a code that occurs via stepwise polymerization, like all major macromolecules. In respects to DNA, it is Nucleic Acid sequences that polymerize to create the DNA. In eukaryotic cells this happens at multiple replicons (regions of replication). So you can look DNA as code for itself. You also have rRNA, mRNA, and tRNA. All of these code for and do specific things. rRNA facilitates the creation and movement of the ribosome, where mRNA and tRNA "code" for the final protein. tRNA serves as the principle code strand for the correct Amino Acids. This is read as a series of three N.A's (codons) One codon for a respective Amino Acid. mRNA actually guides the synthesis of these polypeptide chains. You also have something called operons. These are groups of genes with related functions that are clustered together. This allows for rapid initiation and termination of gene expression. Im sure there are a few others but these are those that come off the top of my head. The term "code" and molecular bio are very much intertwined.
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$\begingroup$ I answered the question before his edit $\endgroup$ Commented Jan 3, 2015 at 7:08
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$\begingroup$ Yea in respects to these situations rather than editing my answers I'll leave them as they are. And comment if I see fit. The only other situation where a "code" would represent its intrinsic definition would be with operons and genomic expressions. $\endgroup$ Commented Jan 3, 2015 at 7:12
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$\begingroup$ I thought this was a nice answer for how I phrased the question previously. Your answer isn't what I had intended the original question to imply. Hence I changed it immediately. But had I meant to ask that particular question, this answer would have been succinct and sufficient. I am new to SE, so if there is a better way to edit questions in the future I am open to suggestions. I would have liked to retain the information in how I phrased it originally so that your answer wouldn't seem so unrelated to the current phrasing. $\endgroup$ Commented Jan 3, 2015 at 8:49
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$\begingroup$ wait, is the lac operon an operon of the type you mentioned? I don't remember much about it, but i remember learning about that in my intro bio class $\endgroup$ Commented Jan 3, 2015 at 21:27
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$\begingroup$ Yep Lac Operon is a good introduction to the functioning and mechanisms behind operons. I also first heard of the Lac Operon in my Cell and molecular bio undergrad course $\endgroup$ Commented Jan 4, 2015 at 23:03
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I am not very familiar with them, but I hear that bacterial non-ribosomal peptide synthases are made of catalytic modules, lined up in series, paralleling their product. My suspicion is that there is some promiscuity / ambiguity in the nonribosomal code.
Also, N-glycosylation in the ER / Golgi occurs in a defined series of events, but that includes backtracking (that is, sugar cleavage), which I am not sure would belong in a finite state machine.
